Merge pull request ome#14 from sbesson/6.2.0-m1

CZI fix
snoopycrimecop · Aug 5, 2019 · 5ecfb57 · 5ecfb57
2 parents c0f1255 + aa806eb
commit 5ecfb57
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Showing 2 changed files with 9 additions and 5 deletions.
diff --git a/components/formats-gpl/src/loci/formats/in/DeltavisionReader.java b/components/formats-gpl/src/loci/formats/in/DeltavisionReader.java
@@ -852,10 +852,6 @@ protected void initExtraMetadata() throws FormatException, IOException {
       }
 
       store.setImageDescription(imageDesc, series);
-
-      if (timestamp != null) {
-        store.setImageAcquisitionDate(new Timestamp(timestamp), series);
-      }
     }
 
     populateObjective(store, lensID);
@@ -871,6 +867,14 @@ protected void initExtraMetadata() throws FormatException, IOException {
         }
     }
 
+    // timestamp stored in the .dv file takes precedence
+    // over the timestamp in the log file
+    if (timestamp != null) {
+      for (int series=0; series<getSeriesCount(); series++) {
+        store.setImageAcquisitionDate(new Timestamp(timestamp), series);
+      }
+    }
+
     if (xTiles * yTiles > getSeriesCount()) {
       if (xTiles == getSeriesCount()) {
         yTiles = 1;

diff --git a/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java b/components/formats-gpl/src/loci/formats/in/ZeissCZIReader.java
@@ -2136,7 +2136,7 @@ private void translateInformation(Element root) throws FormatException {
           }
           if (positions.getLength() == 0 && (mosaics <= 1 || (prestitched != null && prestitched))) {
             positions = scene.getElementsByTagName("CenterPosition");
-            if (positions.getLength() > 0) {
+            if (positions.getLength() > 0 && nextPosition < positionsX.length) {
               Element position = (Element) positions.item(0);
               String[] pos = position.getTextContent().split(",");
               positionsX[nextPosition] = new Length(DataTools.parseDouble(pos[0]), UNITS.MICROM);